What happens when I press F while selecting two faces?
What happens for real is a mega-super-wonky N-gon is created using all the vertices that are selected. F activates the fill tool, it appears to be vertex driven, that means it does recognize when a face is selected, just that there are four more vertices; hitting F forces blender to try to create a new face with all the vertices you selected as its extremities.

Lets assume that you were using nice, clean mesh, only quads. After selecting two faces, filling them 


destroys the old faces
form a new 6-8 vertex face (depending on whether or not the faces were adjacent)
places the origin of the new face at the average of the vertices.


Now, I guess, this is essentially merging the two faces, but its bad form because it causes those dreaded N-gons, and you can see here what the results will be like when the faces aren't flush: